Most library preparation pipelines have been automated to increase robustness and cost efficiency.

Libraries can be sequenced in either single-read of paired-end formats and for read lengths of 50, 100, 150, or 250 bases (up to 300 bases for the MiSeq). On average, 15 M reads can be obtained on the MiSeq and from 150M to over 450M reads can be obtained on a single lane of HiSeq flowcell depending on the sequencing mode selected.

Sequences can be downloaded directly from Nanuq. Sequence reads will be delivered as BAM files for human, rat and mouse and as fastq for the other species.